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Roy's email (and bioperl.org not bioperl.edu)
2008-12-08
cjfields
Roy's
em
a
il
(and bioperl
.
org not
b
ioper
l
.
edu)
commit
|
commitdiff
|
tree
2008-12-08
c
jfields
Up
d
ate
d
emails
commit
|
commitdiff
|
tree
2008-12-07
c
j
f
i
e
lds
[
bug 2
6
99]
commit
|
commitdiff
|
tree
2008-12-05
cj
f
ields
Need to
r
et
r
ieve the
t
ree for
o
utpu
t
commit
|
commitdiff
|
tree
2008-12-05
cjf
i
elds
[
bu
g
2450]
commit
|
commitdiff
|
tree
2008-12-04
cjfields
Mak
e
Target a true DBLink
commit
|
commitdiff
|
tree
2008-12-04
cjf
i
elds
Directory is no longer needed (Heik
k
i
split this up
.
.
.
commit
|
commitdiff
|
tree
2008-12-03
cjfield
s
add for
c
e_nse tests
commit
|
commitdiff
|
tree
2008-12-03
cjf
i
elds
leave I
D
undefined
if it i
s
n't present, but allow the
.
.
.
commit
|
commitdiff
|
tree
2008-12-03
cjfields
Remove f
i
l
es
accidently
added
f
r
o
m last c
o
mmit
commit
|
commitdiff
|
tree
2008-12-03
c
j
fields
R
eor
g
anize Tools tests (
n
ee
d
s some mo
r
e splitting)
commit
|
commitdiff
|
tree
2008-12-03
cjfield
s
Remove (tests are r
e
dundant
,
in Consed
.
t)
commit
|
commitdiff
|
tree
2008-12-03
cjfields
Merge te
s
ts and remove r
e
dunda
n
t file
commit
|
commitdiff
|
tree
2008-12-03
cjfiel
d
s
U
pdate test count
commit
|
commitdiff
|
tree
2008-12-03
c
jfiel
d
s
M
erge
tes
t
s
commit
|
commitdiff
|
tree
2008-12-03
cjfi
e
lds
Remove r
e
du
n
dant
fi
l
e
commit
|
commitdiff
|
tree
2008-12-03
cjfields
Rem
o
ve old files
commit
|
commitdiff
|
tree
2008-12-03
c
jfields
Star
t
To
o
ls move
commit
|
commitdiff
|
tree
2008-12-03
cj
f
ields
small updates:
commit
|
commitdiff
|
tree
2008-12-03
cjfields
f
orgot to i
n
c
r
e
ment test
c
ou
n
t
commit
|
commitdiff
|
tree
2008-12-03
c
j
f
i
elds
Ad
d
a coupl
e
of te
s
ts for seq_i
d
(small but significa
n
t
.
.
.
commit
|
commitdiff
|
tree
2008-12-02
cj
f
ields
[
bug 2450]
commit
|
commitdiff
|
tree
2008-12-02
cjfi
e
lds
[bug 2450]
commit
|
commitdiff
|
tree
2008-12-02
cjfields
[bug 2450]
commit
|
commitdiff
|
tree
2008-12-02
c
jfie
l
ds
[bug 2450]
commit
|
commitdiff
|
tree
2008-12-02
cjfields
some pod updates
commit
|
commitdiff
|
tree
2008-12-02
c
j
fields
[bu
g
2450]
commit
|
commitdiff
|
tree
2008-12-02
cjfi
e
lds
fix
e
rrone
o
usly
r
e
named stockhol
m
tests
commit
|
commitdiff
|
tree
2008-12-02
cjfields
small pod fix
commit
|
commitdiff
|
tree
2008-11-30
cjfields
silen
c
e Gu
e
ssSeqF
o
rmat
.
t warn
i
ngs
(
not s
u
re if old
.
.
.
commit
|
commitdiff
|
tree
2008-11-28
cjfields
rearrang
e
to
a
void
unnecessary warnin
g
s
commit
|
commitdiff
|
tree
2008-11-28
cj
f
ields
A
d
d
w
a
r
ning for missin
g
data (real
b
ug)
commit
|
commitdiff
|
tree
2008-11-28
cjfield
s
hash
r
ef, not a hash
commit
|
commitdiff
|
tree
2008-11-28
c
jfields
tes
t
file nam
e
and test #
c
orrection
commit
|
commitdiff
|
tree
2008-11-28
c
jfi
e
l
d
s
c
or
r
ect test file name
commit
|
commitdiff
|
tree
2008-11-28
cj
f
ields
'::', n
o
t ':'
commit
|
commitdiff
|
tree
2008-11-28
cjfields
r
e
name (recurs
i
ve
te
s
t
s
think this is a test fil
e
)
commit
|
commitdiff
|
tree
2008-11-28
cjfields
recur
s
e into
t
e
s
t subdirectories (means any non-test
.
.
.
commit
|
commitdiff
|
tree
2008-11-28
cjfields
r
e
m
o
ve red
u
ndant copy
commit
|
commitdiff
|
tree
2008-11-28
cjfields
move
i
nt
o
directo
r
y structu
r
e
commit
|
commitdiff
|
tree
2008-11-28
cj
f
ield
s
move into dir
e
ct
o
ry stru
c
t
ure (Da
v
eM++)
commit
|
commitdiff
|
tree
2008-11-26
cj
f
ields
[bu
g
2567]
commit
|
commitdiff
|
tree
2008-11-26
cjfields
Redunda
n
t
; f
i
l
e
was renamed S
e
ar
c
h
I
O
_
b
last_pull
.
t
.
commit
|
commitdiff
|
tree
2008-11-26
cjfields
[bug
2686]
commit
|
commitdiff
|
tree
2008-11-26
cjfiel
d
s
fix
s
ubve
r
s
ion
tags
commit
|
commitdiff
|
tree
2008-11-25
cjfie
l
ds
po, not poa
commit
|
commitdiff
|
tree
2008-11-25
cjfi
e
ld
s
f
ix undefined value wa
r
nin
g
s
commit
|
commitdiff
|
tree
2008-11-25
cjfield
s
[bug
2
6
86]
commit
|
commitdiff
|
tree
2008-11-25
cjfields
[bug 2641, 2642]
commit
|
commitdiff
|
tree
2008-11-25
cjfie
l
ds
split up AlignIO tes
t
s
commit
|
commitdiff
|
tree
2008-11-25
cjfields
[bug 26
8
2]
commit
|
commitdiff
|
tree
2008-11-25
cjfields
[bug 2630]
commit
|
commitdiff
|
tree
2008-11-24
cjfields
[
b
ug 2633]
commit
|
commitdiff
|
tree
2008-11-24
cj
f
ields
[bug 2663]
commit
|
commitdiff
|
tree
2008-11-24
cjfields
[bug
2663
]
commit
|
commitdiff
|
tree
2008-11-24
c
jfie
l
ds
[bug 263
0
]
commit
|
commitdiff
|
tree
2008-11-24
c
j
fields
[
bug 2
2
62
]
commit
|
commitdiff
|
tree
2008-11-24
c
j
fie
l
d
s
[bug
2
630]
commit
|
commitdiff
|
tree
2008-11-18
cjf
i
e
l
ds
* Double-checked data,
t
est
e
d results were wrong
commit
|
commitdiff
|
tree
2008-11-18
c
j
fields
* seq_i
n
ds is
not defined
for Model-based H
S
Ps
commit
|
commitdiff
|
tree
2008-11-18
cjfields
* fix POD
commit
|
commitdiff
|
tree
2008-11-17
cjfields
* 'highly' (and I g
e
t
r
15000!)
commit
|
commitdiff
|
tree
2008-11-17
c
jfie
l
ds
Remove redundan
t
test files
commit
|
commitdiff
|
tree
2008-11-17
c
j
fields
[test
s
]
commit
|
commitdiff
|
tree
2008-11-17
cjfields
mo
v
e results2ha
s
h test utility sub
t
o SearchUtils
commit
|
commitdiff
|
tree
2008-11-16
c
j
f
i
elds
[bug 266
3
]
commit
|
commitdiff
|
tree
2008-11-16
cj
f
ield
s
perltidy
commit
|
commitdiff
|
tree
2008-11-16
cjfields
[bug 2
6
3
5]
commit
|
commitdiff
|
tree
2008-11-14
c
jfield
s
[bug 2656]
commit
|
commitdiff
|
tree
2008-11-11
c
j
fiel
d
s
remove
d
ebugging
lines
commit
|
commitdiff
|
tree
2008-11-11
cjfields
re
m
ove fix
e
d verb
o
se flag
commit
|
commitdiff
|
tree
2008-11-11
c
jf
i
elds
[bug 2650]
commit
|
commitdiff
|
tree
2008-11-11
cjfields
Cl
a
ri
f
y result_c
o
unt
(
discussions on ma
i
l
l
ist pe
r
.
.
.
commit
|
commitdiff
|
tree
2008-11-11
cj
f
ie
l
ds
[bu
g
2632]
commit
|
commitdiff
|
tree
2008-11-10
cjfields
[bug
264
5
]
commit
|
commitdiff
|
tree
2008-11-04
cjfields
wrap text
commit
|
commitdiff
|
tree
2008-11-04
cj
f
i
eld
s
* parse
'
F
e
a
t
ure
s
i
n this part
o
f
subject
sequence
.
.
.
commit
|
commitdiff
|
tree
2008-11-04
cjfields
*
pars
e
'Features in th
i
s part of
subject se
q
u
ence
.
.
.
commit
|
commitdiff
|
tree
2008-10-30
cjfields
[bug 2
6
32]
commit
|
commitdiff
|
tree
2008-10-29
cjfields
fix seq_ind
s
(); wasn't calling identical
resi
d
u
es for
.
.
.
commit
|
commitdiff
|
tree
2008-10-29
cjf
i
elds
[bug
2633]
commit
|
commitdiff
|
tree
2008-10-28
cjfi
e
lds
[bug 2630
]
commit
|
commitdiff
|
tree
2008-10-26
cjfields
Fix unlink() warning
commit
|
commitdiff
|
tree
2008-10-26
cjfields
end
= s
t
a
rt if only
star
t
is pa
s
se
d
commit
|
commitdiff
|
tree
2008-10-26
cjf
i
el
d
s
use val
i
d_Location to check
L
ocation state
commit
|
commitdiff
|
tree
2008-10-26
cjf
i
elds
add docs for Locati
o
nI
met
h
od va
l
id
_
Locat
i
on
commit
|
commitdiff
|
tree
2008-10-26
cj
f
i
elds
[bug 2
6
21]
commit
|
commitdiff
|
tree
2008-10-26
c
j
fields
[
b
ug 2
6
21]
commit
|
commitdiff
|
tree
2008-10-26
cjfields
[
b
ug
2
62
4
]
commit
|
commitdiff
|
tree
2008-10-26
c
jfields
[bug 2621]
commit
|
commitdiff
|
tree
2008-10-25
cjfield
s
b
u
llet-
p
r
o
of prototype test
commit
|
commitdiff
|
tree
2008-10-22
c
jfield
s
fix file properties
commit
|
commitdiff
|
tree
2008-10-22
cjfields
n
ew module for parsi
n
g vec
s
creen -f 3 output, co
u
r
tesy
.
.
.
commit
|
commitdiff
|
tree
2008-10-15
cjfields
a
d
d -source fo
r
ARP
commit
|
commitdiff
|
tree
2008-10-15
cjfields
[bug 2563]
commit
|
commitdiff
|
tree
2008-10-10
cjfiel
d
s
typo
commit
|
commitdiff
|
tree
2008-10-10
cjf
i
elds
[bug 2519]
commit
|
commitdiff
|
tree
2008-10-10
cj
f
i
e
l
ds
[bug 2519]
commit
|
commitdiff
|
tree
2008-10-07
cjfields
ad
d
svn t
a
g
commit
|
commitdiff
|
tree
2008-10-07
cjfields
TODO
'
s
work
commit
|
commitdiff
|
tree
next